The security partnership that the United States and Pakistan developed following the events of September 11, 2001, is one of the most consequential and controversial bilateral relationships in the 21st century. This paper represents an in-depth analysis of the way in which the restructured alliance based on mutual military assistance and engagement in the war on terrorism conditions the intra-Pakistani political stability. The paper explores the foreign security alliances, military authority entrenchment, development of the governance systems, militant uprising, and changes in public opinion. It brings into view the paradoxical consequences: on the one hand, this alliance contributes to the increase of survival chances and operational capabilities of the state, yet on the other hand, it strengthens the political vulnerability, the pattern of civil-military imbalance, and extreme polarization of the society.